Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Prediction of boiling flow characteristics in rough and smooth microchannels using molecular dynamics simulation: Investigation the effects of boundary wall temperatures

Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches.

Molecular dynamics simulation of Couette and Poiseuille Water-Copper nanofluid flows in rough and smooth nanochannels with different roughness configurations

The molecular dynamics simulation of thermal manner of Ar/Cu nanofluid flow: The effects of spherical barriers size

Molecular dynamic simulation to study the effects of roughness elements with cone geometry on the boiling flow inside a microchannel

The effects of suspending Copper nanoparticles into Argon base fluid inside a microchannel under boiling flow condition by using of molecular dynamic simulation

This paper presents molecular dynamics simulations to study on the effects of external driving force and boundary wall temperature on the density, velocity and temperature profiles of Argon fluid atoms, flowed in a platinum microchannel with square section. The Argon atoms are structured in three regions. Two thin liquid film of Argon sandwich central vapor zone. Applying wall temperatures in the range of 84K to 133K prepares boiling condition which causes liquid atoms move from lateral layers to central bins of microchannel. Afterward, density of central layers of microchannel increases which is highlighted by sampling data after equilibrium condition of system energy in 4 time steps. It is concluded that augmentation of external driving forces on the Argon atoms from 0.002 to 0.01 and 0.02 eV/Angstrom can increase flow temperature from 180K to 1920K and 7570K, respectively which is noticeable for practical application such as medical especially in Cryosurgery. Moreover, augmentation of external forces can increase velocity profiles of Argon fluid flow. Generally, density was independent from variation of external force and boundary wall temperature in the studied limits. Also, alteration of boundary wall temperature does not play very important role on the velocity and temperature of Argon fluid inside microchannel.

A statistical method for simulation of boiling flow inside a Platinum microchannel

Impact of dust concentration and weather conditions – wind speed and relative humidity – on power generation of photovoltaic (PV) panels investigated experimentally in Tehran, Iran, for the period ...

Hossein Ahmadi-Danesh-Ashtiani

Papers

Molecular dynamic simulation to study the effects of roughness elements with cone geometry on the boiling flow inside a microchannel

The effects of suspending Copper nanoparticles into Argon base fluid inside a microchannel under boiling flow condition by using of molecular dynamic simulation

A statistical method for simulation of boiling flow inside a Platinum microchannel

Effect of dust concentration, wind speed, and relative humidity on the performance of photovoltaic panels in Tehran

Comparative study on the multistage solar still performance utilizing PCM in variable thicknesses